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−臨 床 血 液− The 75th Annual Meeting of the Japanese Society of Hematology Myeloid neoplasms:CML, MPN, MDS, and others EL-21 Topics A novel BIM deletion polymorphism: implications and lessons for cancer targeted therapies Sheila SOH 1, S. Tiong ONG 1, 2, 3, 4 Key words : Genetic polymorphism, Targeted therapy, Response heterogeneity, Drug resistance are functionally important, understanding their mecha- Introduction Molecularly targeted therapy has revolutionized cancer therapy, and resulted in consistently high response rates, nism of action may also provide novel therapeutic approaches to prevent and/or treat clinical resistance. Toward this end, we outline our recent discovery of a often associated with improvements in progression free common polymorphism in the BIM gene that accounts for survival (PFS) as well as improved overall survival (OS)1). heterogeneous responses in at least two human cancers, These advances have benefited many patients suffering chronic myeloid leukemia (CML) and epidermal growth from cancers previously considered to be highly therapy factor receptor-mutated non-small-cell lung cancer (EGFR 2, 3) resistant . Such advances are based on the ability to NSCLC), and the lessons we have learned from it4). identify the molecular drivers of each cancer, and With over a decade of experience in many such cancer The BIM deletion polymorphism and intrinsic resistance to targeted therapies models, we have begun to appreciate that a major issue To identify structural variations (SVs) that were facing the field is the degree of response heterogeneity associated with tyrosine kinase inhibitor (TKI) resistance observed across different cancers even when they in CML patients, we used DNA sequencing of paired-end molecularly defined and targeted. This heterogeneity ditags (DNA-PET) to sequence and compare the ge- encompasses significant variations in depth of response to nomes of three TKI-resistant patients with those of two initial therapy, duration of response, and OS. A major TKI-sensitive patients. From the list of SVs that occurred challenge will be to understand the basis for tumor and exclusively in the TKI-resistant patients, one candidate patient heterogeneity, and to overcome suboptimal stood out. This SV was a 2.9 kb deletion that occurred in responses so that all individuals with cancer can enjoy intron 2 of the BIM (otherwise known as BCL2L11) gene. optimal responses. Increased knowledge in this area will This was of tremendous interest to us given the well- lead to improved biomarkers for predicting resistance, known role of BIM in mediating TKI-induced apoptosis in and disease transformation. Further, if these biomarkers a number of cancers 5). Targeted sequencing of the BIM specifically target those drivers pharmacologically. locus revealed that the same deletion was found in all 1 Cancer & Stem Cell Biology Signature Research Programme, Duke-NUS Graduate Medical School, Singapore 2 Department of Haematology, Singapore General Hospital, Singapore 3 Department of Medical Oncology, National Cancer Centre, Singapore 4 Division of Medical Oncology, Department of Medicine, Duke University Medical Center Durham, NC, USA (1714)168 three samples, suggesting germline origin. This was confirmed when we screened a large cohort of normal individuals and found that it occurred at a frequency of 12.3% in East Asian populations, but was absent in African or European populations. Clinically, a retrospective analysis of an East Asian TKI-treated CML cohort revealed an increased risk for resistant disease as defined by 臨 床 血 液 54:10 European Leukemia Net criteria (OR/2.94, p/0.02, 95% heterogeneity may be classified as either acquired and CI/1.17─7.43) in patients with the polymorphism. somatic, or inherited and germline. Here, it should be We went on to show that the deletion results in a switch appreciated that germline variants may also influence the in splicing patterns to favor the production of exon 3- likelihood of the acquisition of acquired mutations that containing BIM isoforms. Because exon 3 and 4 are confer resistance, as discussed in more detail below. spliced in a mutually exclusive fashion, exon 3-containing Examples of acquired mutations are those that directly isoforms lack the BH3 domain that is found in exon 4 and mediate resistance to targeted therapies by interfering is required for pro-apoptotic function. To prove that the with the binding of the drug to the active site of the target polymorphism was sufficient to confer resistance to TKIs, enzyme. These mutations are thought to arise stochasti- we introduced it into the K562 cell line using zinc finger cally in a tumor cell subclone, and as might be expected, nuclease technology. We demonstrated that the increase have been described to pre-exist the use of the targeted in exon 3 to exon 4 ratio was recapitulated in the deletion- drug7). Examples of germline variants that directly containing clones and that apoptosis was attenuated in a mediate resistance to targeted therapies are much rarer. polymorphism dose-dependent manner. Using the same More commonly, these variants have an indirect effect, approach, we validated our in vitro findings in another and usually affect pharmacologic parameters8). These kinase-driven cancer, EGFR NSCLC, and showed that pa- include polymorphisms that either modulate drug metabo- tients with EGFR NSCLC had inferior progression-free lism or drug import/export, and thereby cause resistance survival (PFS) of 6.6 vs 11.9 months when compared to by modulating intracellular drug concentrations. We also patients without the deletion polymorphism. Notably, we consider the situation where germline variants may were able to overcome resistance mediated by the enhance the likelihood of a tumor acquiring secondary polymorphism by using ABT-737, a BH3 mimetic6), to mutations. In the case of the BIM deletion polymorphism, pharmacologically restore BIM function in our genome- it is possible that suboptimal doses of TKIs may allow edited lines as well as primary samples with the deletion. subclones of tumor cells to survive, proliferate, and accumulate secondary mutations that themselves confer Assessing causes of response heterogeneity in cancer targeted therapies TKI resistance. Recent reviews have classified clinical resistance to Response heterogeneity is a broad term, and can targeted therapies as being primary or secondary9). The include the quality of the initial response to targeted latter are defined as patients who fail to achieve any therapy, PFS, and OS. In hematologic malignancies, response to initial therapy, while the former are those who including CML, the depth of response is routinely have an initial response but who subsequently relapse or measured by standard quantitative laboratory tests (e.g. progress. Frequently, the causes of primary and secon- quantitative RT-PCR for BCR-ABL1 transcripts), which dary clinical resistance are attributed to germline and serve as a useful and objective measure of initial response. acquired mutations respectively. However, it should be In solid tumors, molecularly-based quantitative measures appreciated that this segregation assumes that germline are more challenging to assess, and in practical terms mutations confer absolute drug resistance, which may not responses are usually limited to measuring best tumor be the case, especially since tumor populations are known responses by imaging modalities. Accordingly, other to be genetically heterogeneous10). This concept will be surrogate measures of response are frequently used such discussed further below. as PFS and OS. However, OS especially can be subject to Study design is also critical to the efficient discovery of confounding factors since progressing patients are usually genetic variants mediating response heterogeneity8). First treated with alternative therapies including cytotoxic of all, such studies should be sufficiently powered to chemotherapy and radiotherapy. Thus, when response detect variants of clinical significance and be independent- heterogeneity is assessed it should be specific to the ly validated. Secondly, when using genome-wide ap- clinical measure being assessed. In the case of EGFR proaches to identify variants associated with response NSCLC, one possible objective clinical measure is the best heterogeneity, it is important to consider the population response on CT scans. being studied to enable efficient discovery. As far as In the broadest sense, the genetic causes for response possible, the study should include homogenous popula169(1715) −臨 床 血 液− tions, and in the ideal situation, use a single molecularly played by several groups in clearly and convincingly defined entity, e.g. EGFR-mutated non-small cell lung demonstrating the critical importance of BIM expression cancer, treated with a single agent. Further, if the study is in determining sensitivity to TKIs in CML12, 13), and the to identify resistance to targeted therapies, then those second was the availability of several East Asian CML cell populations should have been treated only with that agent, lines, one of which (KCL22) was found to harbor the BIM otherwise confounding factors will likely be introduced deletion polymorphism and to be intrinsically resistant to since resistance and/or sensitivity to different therapeutic TKIs14). Here, it should be noted that the latter are almost agents is likely to be multifactorial. exclusively Japanese in origin, and we owe a debt of gratitude to investigators in the past for their contribution Discovery of the BIM deletion polymorphism to our studies. The impetus for the work that led to the discovery of the BIM deletion polymorphism was to uncover mechanisms Lessons from the discovery of the BIM deletion that mediated intrinsic resistance to ABL1 kinase inhibi- One of the most important lessons we learnt from the tors in CML. Prior work had suggested that a significant discovery of the BIM deletion polymorphism is the proportion of individuals with clinical resistance may not potential for relatively common polymorphisms to contrib- harbor mutations in BCR-ABL1, particularly those in early ute significantly to clinical outcome in cancer therapies. stage disease11). Further, studies in such patients indicat- This is likely to due to the critical importance that BIM ed that downstream signalling could still be inhibited by plays in mediating cancer cell death. Indeed, cancer cells TKIs, yet they experienced suboptimal responses11). (as well as normal cells) are exquisitely sensitive to BIM Together, these observations suggested that BCR-ABL1- levels, such that gene dosage effects are clearly seen in independent factors could be underlying resistance. animal models of cancer15). However, the BIM deletion Accordingly, when selecting CML samples for genomic polymorphism is not a perfect predictor of resistance, studies, we deliberately chose material from patients who since the odds ratios of an individual with the deletion had overt clinical TKI resistance but did not harbor BCR- polymorphism being resistant, while robust and clinically ABL1 kinase domain mutations. meaningful, were in the range of 2-3-fold. Thus, the A second feature of our workflow was to include deletion polymorphism likely works in concert with other polymorphic variants as genes of interest, particularly factors, yet to be defined, to determine the ultimate those that were enriched in the study population, i.e. outcome of resistance vs sensitivity. enriched in patients with resistance compared to those That the BIM deletion polymorphism is restricted to without. In many cancer genome-wide studies, polymor- persons of East Asian ancestry is also of interest. While phic variants are usually filtered out to increase the some reports have indicated that TKI response rates in chances of identifying functional variants (such as driver CML may be inferior in East Asia compared to the West16), or resistance-conferring mutations) . Such approaches response rates for TKIs in other cancers including EGFR would have discarded the BIM deletion polymorphism. TKIs in EGFR NSCLC are not clearly inferior in the East A third feature of our work was combining the pipeline compared to the West17). This suggests that different of genetic variants of interest with prompt validation in ethnicities may harbor polymorphic variants of at least CML samples segregated according to the phenotype of equivalent effect to that of the BIM deletion. These may of interest. Thus, because the deletion was almost 3kb in course reside in the same gene, or affect other genes in size, PCR primers could be designed to efficiently detect the same or similar pathways. Further, these polymorphic deletion-containing alleles in a single reaction, without variants may not necessarily occur in genic regions, but in necessarily sequencing the PCR products. When these gene regulatory regions such as those described by the data showed that the deletion was enriched in resistant ENCODE project18). populations, functional effects of the deletion polymor- While the discovery was made in CML, the biology and phism were then investigated at the mechanistic level at clinical significance was extended to EGFR NSCLC. Here, the bench. we observed that the deletion mediated intrinsic resist- Finally, two other important factors in the process of ance to EGFR inhibitors in cell lines, and that the deletion discovery should be mentioned. The first was the role shortened the PFS from 11.9 to 6.6 months in patients (1716)170 臨 床 血 液 54:10 without and with the deletion polymorphism respectively. immune surveillance. Given the known effects of BIM Two other groups have since published data regarding the haploinsufficiency on immune cell function23∼25) and the BIM deletion polymorphism in EGFR NSCLC. The first documented anti-leukemia cell effect of T and NK cells26), 19) was by Dr. Seiji YanoBs group from Kanazawa University . this idea certainly offers a plausible explanation for their These investigators discovered a novel EGFR NSCLC cell data. In this respect, it would be interesting to determine if line with the BIM deletion polymorphism, and demon- rates of relapse among allografted CML patients might be strated that it had the expected phenotype comprising different depending on the BIM deletion status of the intrinsic resistance to EGFR TKIs, increased splicing of donor. Additionally, alternative explanations should also BIM exon 3 at the expense of exon 4, and decreased ex- be considered for the findings of Katagiri et al. Given that pression of BH3-containing BIM isoforms. More impor- patients with CML are closely monitored for benchmark tantly, they made the intriguing finding that the histone responses (usually by measuring the proportion of deacetylase inhibitor, vorinostat, is able to restore the Philadelphia chromosome positive cells in blood and/or aberrant splicing of BIM to favor exon 4 over exon 3, bone marrow, as well as by quantitative RT-PCR for BCR- resulting in expression of BH3-containing BIM isoforms, ABL1 transcripts), it could be possible that those and resensitization to EGFR TKIs. As stated by the individuals with suboptimal responses may have had their authors, the exact mechanism by which vorinostat alters TKI doses increased or their TKI changed to more potent BIM splicing remains to be elucidated, although they second generation drugs. Furthermore, it should be noted that effects of vorinostat on mRNA splicing have highlighted that the BIM deletion polymorphism confers previously been described20). In addition to data support- relative and not absolute TKI resistance, and as such, the ing our initial discovery, we also take note of a recent increases in drug dose and/or potency would be expected publication by a group from Korea with contrary results21). to result in increased responses. Because CML progeni- This group performed a retrospective analysis of 197 pa- tors are thought to act as reservoirs for relapse27), another tients with EGFR NSCLC and concluded that several possible explanation could be that the deletion polymor- factors, including the BIM deletion polymorphism, phism modulates leukemia stem cell survival and/or main- treatment type, EGFR genotype, or smoking did not tenance. This possibility is consistent with the inability of predict inferior PFS. Ideally, studies to determine the role clinical tests to reliably detect or quantify residual CML of the BIM deletion polymorphism should be prospective LSCs in patients28), and the recently described reliance of and include large cohorts of patients, and indeed such a CML LSCs on BCL2 family members for maintenance29). study is under way at the National Cancer Centre in Singapore. More work to be done With regard to CML, a small study by Katagiri et al. In addition to CML and EGFR NSCLC, several other from Tokyo Medical University has suggested that the human cancers have been documented to be critically BIM deletion polymorphism might be used as a criterion dependent on BIM for drug sensitivity. These include c- for discontinuation of imatinib in CML22). These authors KIT-driven gastrointestinal tumors (imatinib resistance), determined the incidence of the BIM deletion polymor- JAK2-mutated myeloproliferative disorders (JAK2 inhibi- phism among patients with CML treated with TKIs, and tor resistance), and acute lymphoblastic leukemia (ALL) who had achieved a complete molecular remission (CMR). (steroid resistance)30∼32). It would therefore be important Interestingly, out of 5 patients who were able to remain in to determine if patients with the BIM deletion polymor- CMR 12 months after stopping TKI therapy, all 5 were phism do indeed experience inferior responses to the negative for the deletion. In contrast, out of 8 patients who above agents, and if so, could they be resensitized using achieved CMR and had disease relapse within 12 months drugs that restore BIM splicing patterns or replace BIM of TKI cessation, 3 had the deletion polymorphism. While function. In performing such studies, it should also be the data is not conclusive (given the small number of pa- noted that concurrent therapy, including cytotoxic agents, tients), it is nevertheless very intriguing, and led the may introduce confounding factors. For example, in ALL, authors to suggest that the deletion polymorphism may be two agents which are commonly used in induction therapy influencing relapse rates via affecting the function of T are vincristine and L-asparaginase, and both have been and/or NK cells, which in turn are responsible for described to kill cancer cells by modulating levels of BCL171(1717) −臨 床 血 液− 2 family members33, 34). Thus, any negative clinical effects References of the BIM deletion polymorphism regarding steroid responsiveness may be counteracted by the ability of 1)Jänne PA, Gray N, Settleman J. Factors underlying sensitivity cytotoxics to tip the overall apoptotic threshold toward cell of cancers to small-molecule kinase inhibitors. Nat Rev Drug Discov. 2009; 8: 709-723. death. Because several agents have now been found to reverse TKI resistance conferred by the BIM deletion polymor- 2)Carella AM, Frassoni F, Melo J, et al. New insights in biology and current therapeutic options for patients with chronic myelogenous leukemia. Haematologica. 1997; 82: 478-495. phism, including BH3 mimetic drugs and HDAC inhibi- 3)Schiller JH, Harrington D, Belani CP, et al. Comparison of tors4, 35), it is now important to test these combinations in four chemotherapy regimens for advanced non-small-cell patients. It remains to be seen whether or not such studies lung cancer. N Engl J Med. 2002; 346: 92-98. will include patients without the BIM deletion polymor- 4)Ng KP, Hillmer AM, Chuah CT, et al. A common BIM phism, since in vitro work suggests that patients with and deletion polymorphism mediates intrinsic resistance and without the deletion may both benefit from BH3 mimetic/ inferior responses to tyrosine kinase inhibitors in cancer. Nat TKI combinations. Finally, two other questions have been raised by our discovery. The first relates to the high frequency of the Med. 2012; 18: 521-528. 5)Adams JM, Huang DC, Strasser A, et al. Subversion of the Bcl-2 life/death switch in cancer development and therapy. Cold Spring Harb Symp Quant Biol. 2005; 70: 469-477. deletion polymorphism is in East Asians, and its non- 6)Cragg MS, Harris C, Strasser A, Scott CL. Unleashing the existence in African or Caucasian individuals. Given the power of inhibitors of oncogenic kinases through BH3 known role of BIM in immune cell function, could the mimetics. Nat Rev Cancer. 2009; 9: 321-326. deletion confer a survival advantage against environ- 7)Roche-Lestienne C, Soenen-Cornu V, Grardel-Duflos N, et al. mental pathogens? Second, given the established role of Several types of mutations of the Abl gene can be found in BIM as a tumor suppressor, could it be cooperating with acquired EGFR mutations to transform lung epithelium, and thus explain the increased incidence of EGFR NSCLC in East Asia compared to the West? In summary, the discovery of the BIM deletion chronic myeloid leukemia patients resistant to STI571, and they can pre-exist to the onset of treatment. Blood. 2002; 100: 1014-1018. 8)Wheeler HE, Maitland ML, Dolan ME, Cox NJ, Ratain MJ. Cancer pharmacogenomics: strategies and challenges. Nat Rev Genet. 2012; 14: 23-34. polymorphism has helped us to understand how germline 9)Mauro MJ. Defining and managing imatinib resistance. variants affecting key genes regulating cell survival and Hematology Am Soc Hematol Educ Program. 2006; 2006: death can have profound effects in the cancer clinic. The discovery has also explained in part why heterogeneous responses to targeted cancer therapies occur, even in cohorts of molecular-defined homogenous cancers. Finally, by elucidating how the BIM deletion impairs the 219-225. 10)Navin N, Kendall J, Troge J, et al. Tumour evolution inferred by single-cell sequencing. Nature. 2011; 472: 90-94. 11)Kantarjian H, Giles F, Wunderle L, et al. Nilotinib in imatinibresistant CML and Philadelphia chromosome-positive ALL. N Engl J Med. 2006; 354: 2542-2551. apoptotic response to TKIs, we now have an opportunity to 12)Kuribara R, Honda H, Matsui H, et al. Roles of Bim in overcome this resistance not only in CML but also other apoptosis of normal and Bcr-Abl-expressing hematopoietic progenitors. 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